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标题: MIMIC数据库SCI复现课程Day2: 数据提取到数据洗濯 [打印本页]

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作者: 西河刘卡车医    时间: 2024-8-1 00:21
标题: MIMIC数据库SCI复现课程Day2: 数据提取到数据洗濯
 

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  微信公众号：熊大学习社、诺维之舟
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  诺维之舟AI：https://gpt4.nwzz.xyz 可在线使用GPT4
  课程相干资料：
（1）课程资料包罗[DAY1]SCI论文复现全部代码-基于R、PostgreSql/Navicat等软件、SQL常用下令与批处理脚本、课本;[Day2]MIMIC IV常见数据提取代码-基于sql、数据洗濯-基于R课本；[Day3] 待更新[Day4]待更新等。关注公众号“熊大学习社”，复兴“mimic01”，获取全部4天MIMIC复现课程资料链接。
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0 课程的总体框架

• Day1：一、MIMIC数据库零基础入门
  （1）MIMIC数据库获取
  （2）MIMIC数据库软件安装
  （3）MIMIC数据表介绍、基础数据提取
  
• Day2：二、MIMIC数据库数据提取与洗濯
  （1）物化视图安装与简介
  （2）关键数据提取与实操
  （3）数据洗濯实操
  
• Day3：三、MIMIC数据库SCI论文复现上
  （1）MIMIC数据库常用的研究方法
  （2）MIMIC数据库SCI论文分析
  （3）数据提取与洗濯
  
• Day4：四、MIMIC数据库SCI论文复现下
  （1）多模型Logistic回归模型
  （2）限制性立方样条图RCS
  （3）亚组分析
  

这次直播课程的特点：上手操纵+撸代码，零基础到SCI复现，随时互动互换，快速开启你的医学研究。
一、MIMIC IV物化视图

MIMIC IV物化视图怎样安装，物化视图有哪些，主要有什么用？
1 增补：Navicat中的表显示不出来，怎么办？

Navicat的表显示不出来的标题已解决，是版本过低导致的。升级版本即可，已放课程资料包。
2 建立MIMIC IV数据库物化视图

在G:/program files/MIMIC/mimic-code-main/mimic-iv/concepts_postgres（你的SQL下令文件夹）目次下运行cmd.

1.  # 访问数据库
2.  psql -U postgres -p 5432
3.  ​
4.  # 进入mimiciv数据库
5.  \c mimiciv
6.  ​
7.  # 生成函数
8.  \i 'postgres-functions.sql'
9.  ​
10.  # 视图
11.  \i 'postgres-make-concepts.sql'

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看一下postgres-make-concepts.sql
 

里面用的是相对路径，这就是为什么要在上面指定的目次。
 

mimiciv_derived版块其实是在mimic_hosp及mimic_icu两个模块基础上然后在MIMIC数据库官网下载其提供的可视图化代码，然后运行而得出来的61个视图表。
 

也可通过下令行查看。

1.  -- 查看视图
2.  SELECT * FROM information_schema.views;
3.  ​
4.  -- 查看物化视图
5.  SELECT mv.relname AS materialized_view,
6.         pg_get_viewdef(mv.oid) AS definition
7.  FROM pg_class mv
8.  WHERE mv.relkind = 'm';

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从上面的下令行运行结果发现，有报错信息。最后天生的物化视图58个，还缺3个：icustay_hourly、sofa、sepsis3。
 

报错的标题是UNNEST函数不存在。改写代码，不用UNNEST函数实现。
icustay_hourly.sql的代码改写后如下：

1.  -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
2.  DROP TABLE IF EXISTS mimiciv_derived.icustay_hourly; CREATE TABLE mimiciv_derived.icustay_hourly AS
3.  /* This query generates a row for every hour the patient is in the ICU. */ /* The hours are based on clock-hours (i.e. 02:00, 03:00). */ /* The hour clock starts 24 hours before the first heart rate measurement. */ /* Note that the time of the first heart rate measurement is ceilinged to */ /* the hour. */ /* this query extracts the cohort and every possible hour they were in the ICU */ /* this table can be to other tables on stay_id and (ENDTIME - 1 hour,ENDTIME] */ /* get first/last measurement time */
4.  WITH all_hours AS (
5.    SELECT
6.      it.stay_id,
7.      CASE
8.        WHEN DATE_TRUNC('HOUR', it.intime_hr) = it.intime_hr
9.        THEN it.intime_hr
10.        ELSE DATE_TRUNC('HOUR', it.intime_hr) + INTERVAL '1 HOUR'
11.      END AS endtime,
12.      GENERATE_SERIES(-24, CAST(CEIL(EXTRACT(EPOCH FROM it.outtime_hr - it.intime_hr) / 3600.0) AS INT)) AS hrs,
13.      row_number() over (partition by it.stay_id order by it.intime_hr) as rn
14.    FROM mimiciv_derived.icustay_times AS it
15.  )
16.  SELECT
17.    a.stay_id,
18.    CAST(a.hrs AS BIGINT) AS hr,
19.    a.endtime + CAST(b.hrs AS BIGINT) * INTERVAL '1 HOUR' AS endtime
20.  FROM all_hours a
21.  JOIN all_hours b ON a.stay_id = b.stay_id AND a.rn = b.rn;

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进入到三个文件的上一级目次，再运行cmd，然后依次运行sql代码就行。

1.  -- cmd
2.  psql -U postgres -p 5432
3.  ​
4.  -- 进入mimiciv数据库
5.  \c mimiciv
6.  ​
7.  -- 物化视图：demographics/icustay_hourly.sql
8.  \i 'demographics/icustay_hourly.sql'
9.  ​
10.  ​
11.  -- 物化视图：score/sofa.sql
12.  \i 'score/sofa.sql'
13.  ​
14.  -- 物化视图：sepsis/sepsis3.sql
15.  \i 'sepsis/sepsis3.sql'

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3 物化视图

（1）age，年龄

1.  SELECT  
2.    ad.subject_id
3.    , ad.hadm_id
4.    , ad.admittime
5.    , pa.anchor_age
6.    , pa.anchor_year
7.    , mimiciv_derived.DATETIME_DIFF(ad.admittime, mimiciv_derived.DATETIME(pa.anchor_year, 1, 1, 0, 0,0),'YEAR') + pa.anchor_age AS age
8.  FROM mimiciv_hosp.admissions  AS ad
9.  INNER JOIN mimiciv_hosp.patients  AS pa
10.  ON ad.subject_id = pa.subject_id
11.  ;

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这里就使用了官方函数 "mimiciv_derived.DATETIME_DIFF" 和 “mimiciv_derived.DATETIME”， 假如您没有安装官方函数就会报错！
（2）weight_duration，体重变革

weight_duration, ICU期间体重的变革，体重是反应患者营养状态的重要因素。具体代码看物化视图天生所调用的sql文件。
 

（3）GCS， 神经体系功能评分

GCS评分， 神经体系功能评分。
 

二、MIMIC IV数据提取

MIMIC IV的关键数据有哪些，常用提取下令是什么？
1 MIMIC IV关键数据与表格

mimiciv_derived模块的61个视图具有非常多的提取信息，基本上一个入住ICU病人的90%以上的信息都能在这提取！！
除了61个视图，另有15个函数。
 

（1）计算患者的真实年龄

   患者的真实年龄 = anchor_age + admittime - anchor_year
  anchor_age，anchor_year可以在mimiciv_hosp.patients表中找到
患者的入院年龄可以在mimiciv_hosp.admissions表中找到。

• 第一种方法：patients表和admissions表联合查询
  

公式用sql代码体现：

1.  pa.anchor_age + mimiciv_derived.DATETIME_DIFF(ad.admittime,
2.      mimiciv_derived.DATETIME(pa.anchor_year, 1, 1, 0, 0, 0)

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这里就使用了官方函数 "mimiciv_derived.DATETIME_DIFF" 和 “mimiciv_derived.DATETIME”， 假如您没有安装官方函数就会报错！
这个算法算出来的年龄是小数，我们可以使用ROUND函数转成整数，完整SQL如下：

1.  SELECT  ad.subject_id,  
2.  MAX (ROUND(pa.anchor_age + mimiciv_derived.datetime_diff ( ad.admittime, mimiciv_derived.DATETIME ( pa.anchor_year, 1, 1, 0, 0, 0 ), 'YEAR' ), 0)) AS Age_real
3.  FROM  mimiciv_hosp.admissions AS ad,  mimiciv_hosp.patients AS pa
4.  WHERE  ad.subject_id = pa.subject_id
5.  GROUP BY  ad.subject_id   LIMIT 200;

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第二种方法：物化视图age表

1.  SELECT subject_id, ROUND(age,0) as age
2.  FROM age
3.  LIMIT 100

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（2）排除小于18岁的患者

• 第一种方法
  

先使用子查询先查询出来患者的真实年龄，再排撤除小于18岁的患者。

1. with base as (
2.     SELECT ad.subject_id,
3.     MAX(ROUND(pa.anchor_age + mimiciv_derived.DATETIME_DIFF(ad.admittime,  
4.         mimiciv_derived.DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), 'YEAR'),0)) AS age
5.     FROM mimiciv_hosp.admissions ad, mimiciv_hosp.patients pa
6.     WHERE ad.subject_id = pa.subject_id
7.     GROUP BY ad.subject_id
8. )
9. SELECT * FROM base WHERE base.age >=18 limit 100;

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可以根据代码修改筛选出来其他年龄段的患者。

• 第二种方法
  

1. SELECT subject_id, ROUND(age,0) as age
2. FROM mimic_derived.age
3. WHERE anchor_age >=18
4. LIMIT 100

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（3）首次入院记录

以急性胰腺反复入院的患者为例，仅保留首次入院数据。
MIMIV IV数据库记录了29万个病人的43万条入院记录，但是在做数据分析和提取的时候，通常只必要提取某个病人的首次入院记录。

• 入院时间排序
  

postgres数据库的内置函数ROW_NUMBER，可将患者举行分组，并可以按照入院时间排序。

1. SELECT ADM.SUBJECT_ID, ADM.HADM_ID, ADM.ADMITTIME,
2. -- 分组排序
3. ROW_NUMBER () OVER(PARTITION BY ADM.SUBJECT_ID ORDER BY ADM.ADMITTIME) AS ADMITTIME_RANK
4. FROM MIMICIV_HOSP.ADMISSIONS AS ADM
5. LIMIT 100;

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• 获取首次入院记录
  

利用子查询，过滤出患者的首次入院记录

1. WITH base AS (
2.     SELECT ADM.SUBJECT_ID,  ADM.HADM_ID,  ADM.ADMITTIME,  
3.     ROW_NUMBER () OVER(PARTITION BY ADM.SUBJECT_ID ORDER BY ADM.ADMITTIME) AS ADMITTIME_RANK
4.     FROM MIMICIV_HOSP.ADMISSIONS AS ADM
5. )
6. SELECT * FROM base WHERE base.ADMITTIME_RANK = 1 LIMIT 100;

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（4）首次进ICU记录

• 第一种方法：icustays表
  

一个患者可以多次住ICU，一个subject_id对应着多个icustay_id。研究通常只选择该患者第一次住ICU的记录。
入ICU记录按照intime排序，这样就可以看到每个icustay_id是对应患者的第频频入ICU。

1. -- 每个病人按照进icu时间排序
2. select stay_id,
3. rank() over (partition by subject_id order by intime) as icu_order
4. from icustays

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第二种方法：物化视图icustay_detail

1. -- 每个病人按照进icu时间排序
2. select subject_id, stay_id
3. from icustay_detail
4. where first_icu_stay = 't'

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（5）高血压（hypertension）患者数据

在d_icd_diagnoses查找高血压的ICD编号和版本。

1. -- 高血压的icd
2. SELECT * FROM "D_ICD_DIAGNOSES" WHERE long_title like '%hypertension%'

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结果许多个，具体哪一个呢，照旧哪几个。
 

假如确定高血压的具体种别是Unspecified essential hypertension（原发性高血压），就确定下来了：icd_code=4019, icd_version=9。

1. -- 查看Unspecified essential hypertension的患者
2. SELECT DISTINCT (HADM_ID)
3. FROM MIMICIV_HOSP.DIAGNOSES_ICD
4. WHERE ICD_CODE = '4019' and ICD_VERSION = 9
5. LIMIT 100;

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假如不确定，查看这些高血压相干的疾病分别都多少患者手术。一种思路是选最多最广泛的群体。

1. -- 查看这些高血压相关的疾病分别都多少患者
2. -- 相关疾病保存到hypertension_diseases
3. WITH hypertension_diseases AS (
4.     SELECT icd_code, icd_version FROM D_ICD_DIAGNOSES WHERE long_title like '%hypertension%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, COUNT(*) AS count
8. FROM DIAGNOSES_ICD d
9. JOIN hypertension_diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version ORDER BY count DESC

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• 阅读SQL代码，掌握其中的知识点。
  

一是结果赋值；
二是别名；
三是统计数count等函数，另有sum等；
四是联合查询join on；
五是分组；
六是排序。
 

• 代码不会写怎么办，借助GPT4来助力。
  

提问：有两个表，一个是疾病与其编号和编号版本的表D_ICD_DIAGNOSES。二是患者与疾病编号的表DIAGNOSES_ICD。用sql语言，首先模糊查找高血压hypertension的编号和版本，然后根据查出的多个结果，查询DIAGNOSES_ICD表中这些结果对应的患者数量。
 

 

GPT给出的代码和终极的代码已经很靠近了，稍作调整就可以用！
（6）脓毒症（sepsis）患者数据

• 总结一下，某疾病的病人数据，可用如下通用代码。
  

在前面的代码基础上加上了疾病名称long_title。

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- %疾病名称英文%对应修改！
4.     SELECT icd_code, icd_version, long_title FROM D_ICD_DIAGNOSES WHERE long_title like '%疾病名称英文%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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以脓毒症（Sepsis）为例。

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- Sepsis
4.     SELECT icd_code, icd_version, long_title FROM D_ICD_DIAGNOSES WHERE long_title like '%Sepsis%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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• 百度翻译（上传截图，图文翻译）
  

上传截图到百度翻译。
 

（7）脑梗（cerebral infarction）患者数据

脑卒中，英文stroke

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- stroke
4.     SELECT icd_code, icd_version, long_title FROM MIMICIV_HOSP.D_ICD_DIAGNOSES WHERE long_title like '%stroke%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM MIMICIV_HOSP.DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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发现这个结果不太好，数据量不多，而且不怎么相干。
试试脑梗死，这是脑卒中的一种，英文，cerebral infarction。

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- cerebral infarction`
4.     SELECT icd_code, icd_version, long_title FROM MIMICIV_HOSP.D_ICD_DIAGNOSES WHERE long_title like '%cerebral infarction%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM MIMICIV_HOSP.DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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相干疾病类型挺多，必要筛选一下。前2个V1254、Z8673是个人病史，不相干。最后几个G43501、G43509等是没有脑梗的，不纳入。
 

1. -- 脑梗患者数据
2. SELECT d.subject_id,d.hadm_id
3. from mimiciv_hosp.diagnoses_icd d
4. WHERE d.icd_code in ('43301','43330','43331','43390','43391','G43609','43411',
5. 'I630','I63012','I63013','I6302','I63032','I63033','I63039','I6309','I631',
6. 'I6310','I63111','I63112','I63113','I63139','I632','I6320','I63212',
7. 'I63213','I63219','I6322','I63231','I63232','I6330','I63311','I63312',
8. 'I63319','I6332','I63321','I63322','I63339','I6334','I63341','I63342','I63343','I6339','I6341',
9. 'I63411','I63412','I63413','I63419','I6342','I6343','I63431','I63432','I63433',
10. 'I63441','I63442','I6350','I6351','I63511','I63512','I63513','I6352','I63521','I63529','I6353','I63531','I63532','I63541','I63542','I63549','I6359','I636','I69312','I69314','I69341','I69342','I69359','I69361','I69362','I69363','I69364')

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（8）生命体征信息（身高、体重、BMI）

• 取第一天入住ICU身高
  

1. SELECT i.subject_id,i.stay_id,i.icu_intime,c.charttime charttime_height,c.height
2. FROM mimiciv_derived.icustay_detail i
3. INNER JOIN mimiciv_derived.height c ON  i.subject_id=c.subject_id AND i.stay_id=c.stay_id
4. WHERE c.charttime BETWEEN i.icu_intime AND mimiciv_derived.DATETIME_ADD(i.icu_intime, INTERVAL '24' HOUR)
5. AND c.height is not NULL

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• 第一天入住ICU体重
  

1. SELECT i.subject_id,i.stay_id,i.icu_intime,c.starttime as starttime_weight,c.weight
2. FROM mimiciv_derived.icustay_detail i
3. INNER JOIN mimiciv_derived.weight_durations c ON  i.stay_id=c.stay_id
4. WHERE c.starttime BETWEEN i.icu_intime AND mimiciv_derived.DATETIME_ADD(i.icu_intime, INTERVAL '24' HOUR)
5. AND c.weight is not NULL

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• BMI
  

可用R语言实现。

1. # BMI: bmi = weight_kg / (height_m ** 2)
2. d$BMI <- round(d$weight_kg/(d$height_m/100)**2,2)
3. table(d$weight_kg, useNA = 'ifan')
4. table(d$height_m , useNA = 'ifan')
5. table(d$BMI      , useNA = 'ifan')
6. d1 <- subset(d, is.na(d$BMI))

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后面联合数据合并举行实操。
（9）GCS神经体系功能评分

第一天入住ICU的GCS评分

1. with t1 as(
2. SELECT i.subject_id,i.stay_id,i.icu_intime, g.charttime as charttime_gcs, g.gcs,
3. ROW_NUMBER () OVER(PARTITION BY g.SUBJECT_ID ORDER BY g.charttime) AS CHARTTIME_RANK
4. FROM mimiciv_derived.icustay_detail i
5. INNER JOIN mimiciv_derived.gcs g ON i.stay_id=g.stay_id
6. WHERE g.charttime BETWEEN i.icu_intime AND mimiciv_derived.DATETIME_ADD(i.icu_intime, INTERVAL '24' HOUR)
7. AND g.gcs is not NULL
8. )
9. select * from t1 where CHARTTIME_RANK = 1

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GCS、APS III、SAPS II、OASIS这四个指标在物化视图mimiciv_derived中都有对应的表格。稍作修改就能提取。

• GCS（Glasgow Coma Scale）：格拉斯哥昏迷评分，用于评估患者的意识状态和神经体系功能。该评分体系包罗眼睛反应、言语能力和活动反应等项目，将每个项目的得分相加得出总分，总分越低体现患者的意识状态越低，常用于评估颅脑损伤和中风等疾病的严重程度。
  
• APS III（Acute Physiology Score III）：急性生理学评分III，是一种用于评估重症患者生理状态的评分体系。APS III通过测量患者的生理指标，如血压、心率、呼吸频率等，以及评估患者的年龄、慢性疾病等因素，来评估患者的疾病严重程度和预后。
  
• SAPS II（Simplified Acute Physiology Score II）：简化急性生理学评分II，也是一种用于评估重症患者生理状态的评分体系。SAPS II通过测量患者的生理指标，如血压、体温、血氧饱和度等，以及评估患者的年龄、慢性疾病等因素，来评估患者的疾病严重程度和预后。SAPS II通常用于评估重症监护患者的预后和病情监测。
  
• OASIS（Oxford Acute Severity of Illness Score）：牛津急性疾病严重度评分，是一种用于评估急性疾病患者严重程度的评分体系。OASIS考虑了患者的年龄、生理指标（如血压、呼吸频率等）、病情持续时间等因素，并通过计算得出一个综合评分，用于衡量患者的疾病严重程度和预后。
  
• ICP（Intra Cranial Pressure）：颅内压力，指颅骨内的压力。ICP是衡量颅脑疾病严重程度的重要指标。正常环境下，颅内压力应处于一定的范围内，但在某些环境下，如颅脑损伤、脑肿瘤等，颅内压力可能升高。监测ICP可以提供有关脑功能和血流环境的重要信息，以及引导治疗和防备并发症的发生。
  
• LODS（Logistic Organ Dysfunction Score）：逻辑器官功能紊乱评分，是一种用于评估重症患者多器官功能停滞的评分体系。LODS通过测量患者的生理指标和临床数据，如血压、呼吸频率、血液学指标等，来评估患者器官功能的紊乱程度。该评分体系可用于评估患者的病情严重程度和疾病预后，并用于重症监护和临床研究中。
  

（10）合并症数据

物化视图charlson表为合并症常用数据表，包罗18种疾病和1个指数。
列名称subject_id:病人IDhadm_id: 住院IDage_score:年龄得分myocardial infarct: 心肌梗死congestive_heart_failure: 充血性心力衰竭peripheral_vascular_disease: 外周血管疾病cerebrovascular_disease:脑血管疾病dementia:痴呆症hronic_pulmonary_disease: 慢性肺部疾病heumatic_disease:风湿病charlson entic_ulcer_disease:消化性溃疡病mild liver disease:轻度肝病diabetsithout_.cc:无并发症的糖尿病diabetes with ce:有并发症的糖尿病paraplegia:截瘫renal disease:肾脏疾病malignant_cancer:恶性肿瘤severe_liver_disease: 重度肝病metastatic_solid-tumor:转移性实体痘aids:艾滋病charlson comorbidity index:查尔森共病指数 以Paraplegia(截瘫)、Renal disease(肾脏病)、CCI(charlson_comorbidity_index)为例。

1. SELECT i.subject_id,i.stay_id,i.icu_intime,c.paraplegia,c.renal_disease,c.charlson_comorbidity_index
2. FROM mimiciv_derived.icustay_detail i
3. INNER JOIN mimiciv_derived.charlson c ON i.subject_id=c.subject_id AND i.hadm_id=c.hadm_id

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（11）呼吸衰竭

首先，查询呼吸衰竭的诊断icd-code。呼吸衰竭：respiratory failure。

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- respiratory failure
4.     SELECT icd_code, icd_version, long_title FROM MIMICIV_HOSP.D_ICD_DIAGNOSES WHERE long_title like '%respiratory failure%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM MIMICIV_HOSP.DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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接着，选取ICD编号和版本，提取相应的数据。这里不妨以急性呼吸衰竭（Acute respiratory failure）为例。

1. with t1 as (
2. SELECT d.subject_id,d.hadm_id,
3. case when d.icd_code is not null then 1
4. ELSE 0
5. END AS Respiratory_failure
6. from mimiciv_hosp.diagnoses_icd d
7. WHERE (d.icd_code in ('51851', '51853', '51881', '51883','51884') and d.icd_version=9) OR
8. (d.icd_code in ('J95821', 'J95822', 'J9600', 'J9601','J9602','J9620','J9621','J9622') and d.icd_version=10)
9. )
11. -- 在t1的基础上增加了mimiciv_derived.icustay_detail表中的信息
12. SELECT i.subject_id,i.stay_id,i.icu_intime,t1.Respiratory_failure
13. FROM mimiciv_derived.icustay_detail i
14. LEFT JOIN t1 on t1.subject_id=i.subject_id and t1.hadm_id=i.hadm_id

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（12）肺栓塞

首先，查询肺栓塞的诊断icd-code。肺栓塞：pulmonary embolism。

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- pulmonary embolism
4.     SELECT icd_code, icd_version, long_title FROM MIMICIV_HOSP.D_ICD_DIAGNOSES WHERE long_title like '%pulmonary embolism%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM MIMICIV_HOSP.DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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接着，选取ICD编号和版本，提取相应的数据。
('41519' , 'I2699' , '41511', '41512', 'I2692', 'I2698' , '41513' , 'I2609', 'I2694', 'I2602', 'I2693', '67382')

1. with t1 as (
2. SELECT d.subject_id,d.hadm_id,
3. case when d.icd_code is not null then 1
4. ELSE 0
5. END AS pulmonary_embolism
6. from mimiciv_hosp.diagnoses_icd d
7. WHERE d.icd_code in ('41519' , 'I2699' , '41511', '41512', 'I2692', 'I2698' , '41513' , 'I2609', 'I2694', 'I2602', 'I2693', '67382')
8. )
10. -- 在t1的基础上增加了mimiciv_derived.icustay_detail表中的信息
11. SELECT i.subject_id,i.stay_id,i.icu_intime,t1.pulmonary_embolism
12. FROM mimiciv_derived.icustay_detail i
13. LEFT JOIN t1 on t1.subject_id=i.subject_id and t1.hadm_id=i.hadm_id

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（13）实验室检查指标：红细胞rbc、wbc、plt、hb

• 红细胞(rbc)
  
• 白细胞(wbc)
  
• 血小板(plt, platelet)
  
• 血红蛋白浓度(HB, hemoglobin)
  

这几个指标都在mimiciv_derived.complete_blood_count表中。

1. SELECT i.subject_id,i.stay_id,i.icu_intime,c.charttime,c.rbc, c.wbc, c.platelet, c.hemoglobin
2. FROM mimiciv_derived.icustay_detail i
3. LEFT JOIN mimiciv_derived.complete_blood_count c ON i.subject_id=c.subject_id AND i.hadm_id=c.hadm_id
4. WHERE c.charttime BETWEEN mimiciv_derived.DATETIME_SUB(i.icu_intime, INTERVAL '6' HOUR)
5. AND mimiciv_derived.DATETIME_ADD(i.icu_intime, INTERVAL '24' HOUR)
6. AND c.rbc is not null

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（14）实验室检查指标：血钠、肌酐

• 血钠(sodium)
  
• 肌酐(creatinine)
  
• 葡萄糖(glucose)
  

这两个指标在mimiciv_derived.chemistry表中。

1. SELECT i.subject_id,i.stay_id,i.icu_intime,c.charttime, c.sodium, c.creatinine, c.glucose
2. FROM mimiciv_derived.icustay_detail i
3. LEFT JOIN mimiciv_derived.chemistry c ON i.subject_id=c.subject_id AND i.hadm_id=c.hadm_id
4. WHERE c.charttime BETWEEN mimiciv_derived.DATETIME_SUB(i.icu_intime, INTERVAL '6' HOUR)
5. AND mimiciv_derived.DATETIME_ADD(i.icu_intime, INTERVAL '24' HOUR)

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（15）甘油三脂

首先，甘油三酯的编号，在MIMICIV_HOSP.D_LABITEMS中查找，为51000。

1. SELECT itemid, label FROM MIMICIV_HOSP.D_LABITEMS WHERE label like '%Triglyceride%'

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接着，查找查验表labevents，甘油三酯的检测值。

1. SELECT subject_id, hadm_id, charttime, valuenum
2. FROM mimiciv_hosp.labevents
3. WHERE itemid in ('51000') and valuenum is not null

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继续，获取ICU病人的数据信息。

1. WITH t1 as (SELECT subject_id, hadm_id, charttime, valuenum
2. FROM mimiciv_hosp.labevents
3. WHERE itemid in ('51000') and valuenum is not null)SELECT i.subject_id,i.stay_id,i.icu_intime,t1.charttime charttime_Triglyceride,t1.valuenum TriglycerideFROM mimiciv_derived.icustay_detail iINNER JOIN t1 ON i.subject_id= t1.subject_id AND i.hadm_id=t1.hadm_idWHERE t1.charttime  BETWEEN mimiciv_derived.DATETIME_SUB(i.icu_intime, INTERVAL '6' HOUR) AND mimiciv_derived.DATETIME_ADD(i.icu_intime, INTERVAL '24' HOUR)

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（16）葡萄糖

glucose这个指标在mimiciv_derived.chemistry表中。参考血钠和肌酐的数据提取。
（17）终末期肾功能不全

AKI：急性肾损伤，在在mimiciv_derived.kdigo_stages表中。
aki_stage ：疾病状态，3体现终末期。

1. SELECT i.subject_id,i.stay_id,i.icu_intime,i.first_icu_stay,
2. CASE WHEN c.aki_stage is not null THEN 1
3. ELSE 0
4. END AS end_stage_renal_disease
5. FROM mimiciv_derived.icustay_detail i
6. LEFT JOIN mimiciv_derived.kdigo_stages c ON i.subject_id=c.subject_id AND i.hadm_id=c.hadm_id
7. WHERE c.charttime BETWEEN i.icu_intime AND i.icu_outtime
8. AND c.aki_stage in (3)

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（18）肝硬化

首先，查询肝硬化的诊断icd-code。肝硬化：cirrhosis。

1. -- 相关疾病信息保存到diseases
2. WITH diseases AS (
3.     -- cirrhosis
4.     SELECT icd_code, icd_version, long_title FROM MIMICIV_HOSP.D_ICD_DIAGNOSES WHERE long_title like '%cirrhosis%'
5. )
6. -- 然后，我们可以使用这个子查询来联合查询用户表，并计算指定疾病编号和版本的病人手术数量
7. SELECT d.icd_code, d.icd_version, h.long_title, COUNT(*) AS count
8. FROM MIMICIV_HOSP.DIAGNOSES_ICD d
9. JOIN diseases h ON d.icd_code = h.icd_code AND d.icd_version = h.icd_version
10. GROUP BY d.icd_code, d.icd_version, h.long_title ORDER BY count DESC

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接着，选取ICD编号和版本，提取相应的数据。

1. with t1 as (
2. SELECT d.subject_id,d.hadm_id,
3. case when d.icd_code is not null then 1
4. ELSE 0
5. END AS cirrhosis
6. from mimiciv_hosp.diagnoses_icd d
7. WHERE d.icd_code in ('5712','5715','5716','K703','K7030','K7031','K717','K74','K741','K742','K743',
8.                      'K744','K745','K746','K7460','K7469','P7881')
9. )
10. -- 在t1的基础上增加了mimiciv_derived.icustay_detail表中的信息
11. SELECT i.subject_id,i.stay_id,i.icu_intime,t1.cirrhosis
12. FROM mimiciv_derived.icustay_detail i
13. LEFT JOIN t1 on t1.subject_id=i.subject_id and t1.hadm_id=i.hadm_id

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（19）癌症（恶性肿瘤）

癌症，恶性肿瘤，malignant_cancer，在mimiciv_derived.charlson表中。

1. SELECT i.subject_id,i.stay_id,i.icu_intime,c.malignant_cancer
2. FROM mimiciv_derived.icustay_detail i
3. INNER JOIN mimiciv_derived.charlson c ON i.subject_id=c.subject_id AND i.hadm_id=c.hadm_id

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2 MIMIC IV数据提取实操

从常见的研究主题出发，考虑多个环境的组合。比如高血压患者的血液指标、首次入院时年龄不小于18岁的高血压患者。
（1）首次入院时年龄不小于18岁的患者

• 第一种方法
  

1. WITH BASE0 AS (
2.     SELECT AD.hadm_id,  MAX(ROUND(pa.anchor_age + mimiciv_derived.datetime_diff(ad.admittime,
3.     mimiciv_derived.datetime(pa.anchor_year, 1, 1, 0, 0, 0), 'YEAR'), 0)) AS age
4.     FROM mimiciv_hosp.admissions AS AD, mimiciv_hosp.patients AS PA
5.     WHERE ad.subject_id = pa.subject_id
6.     GROUP BY ad.hadm_id
7.     LIMIT 1000
8. ),
9. BASE1 AS (
10.     SELECT ADM.subject_id, ADM.hadm_id, ADM.admittime,
11.     ROW_NUMBER() OVER( PARTITION BY ADM.subject_id ORDER BY ADM.admittime) AS admittime_rank
12.     FROM mimiciv_hosp.admissions AS ADM
13. )
14. SELECT * FROM BASE0, BASE1
15. WHERE BASE0.age >= 18 AND BASE1.admittime_rank = 1 AND BASE0.hadm_id = base1.hadm_id
16. LIMIT 200;

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• 第二种方法
  

1. WITH base AS (
2.     SELECT ADM.SUBJECT_ID,  ADM.HADM_ID,  ADM.ADMITTIME,  
3.     ROW_NUMBER () OVER(PARTITION BY ADM.SUBJECT_ID ORDER BY ADM.ADMITTIME) AS ADMITTIME_RANK
4.     FROM MIMICIV_HOSP.ADMISSIONS AS ADM
5. )
6. SELECT * FROM base, age
7. WHERE base.ADMITTIME_RANK = 1 AND age.age >= 18 AND base.hadm_id = age.hadm_id
8. LIMIT 100;

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也可把提取的变量名明确。

1. WITH base AS (
2.     SELECT ADM.SUBJECT_ID,  ADM.HADM_ID,  ADM.ADMITTIME,  
3.     ROW_NUMBER () OVER(PARTITION BY ADM.SUBJECT_ID ORDER BY ADM.ADMITTIME) AS ADMITTIME_RANK
4.     FROM MIMICIV_HOSP.ADMISSIONS AS ADM
5. )
6. SELECT base.subject_id, base.hadm_id, base.admittime, base.admittime_rank, ROUND(age.age, 0) as age
7. FROM base, age
8. WHERE base.ADMITTIME_RANK = 1 AND age.age >= 18 AND base.hadm_id = age.hadm_id
9. LIMIT 100;

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（2）首次进ICU时年龄不小于18岁的患者

• 第一种方法
  

1. WITH base AS (
2.     SELECT ICU.SUBJECT_ID,  ICU.STAY_ID,  ICU.intime,  
3.     ROW_NUMBER () OVER(PARTITION BY ICU.SUBJECT_ID ORDER BY ICU.intime) AS ADMITTIME_RANK
4.     FROM MIMICIV_ICU.ICUSTAYS AS ICU
5. )
6. SELECT base.SUBJECT_ID, base.STAY_ID, base.intime, base.ADMITTIME_RANK, ROUND(age.age, 0) as age
7. FROM base, age
8. WHERE base.ADMITTIME_RANK = 1 AND age.age >= 18 AND base.hadm_id = age.hadm_id
9. LIMIT 100;

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• 第二种方法
  

1. -- 用age和icustay_detail两个物化视图
2. select i.subject_id, i.stay_id, ROUND(a.age,0) as age
3. from icustay_detail as i
4. LEFT JOIN age as a
5. ON i.first_icu_stay = 't'and i.hadm_id = a.hadm_id and a.age>=18

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（3）首次入院时年龄不小于18岁的脓毒症患者

1. WITH base AS (
2.     SELECT ADM.SUBJECT_ID,  ADM.HADM_ID,  ADM.ADMITTIME,  
3.     ROW_NUMBER () OVER(PARTITION BY ADM.SUBJECT_ID ORDER BY ADM.ADMITTIME) AS ADMITTIME_RANK
4.     FROM MIMICIV_HOSP.ADMISSIONS AS ADM
5. ),
6. t1 as (
7. SELECT base.subject_id, base.hadm_id, base.admittime, ROUND(age.age, 0)
8. FROM base, age
9. WHERE base.ADMITTIME_RANK = 1 AND age.age >= 18 AND base.hadm_id = age.hadm_id;
10. ),
11. t2 as (
12. -- 查看脓毒症的患者
13. SELECT DISTINCT (HADM_ID)
14. FROM MIMICIV_HOSP.DIAGNOSES_ICD
15. WHERE ICD_CODE = 'A419' and ICD_VERSION = 10
16. )
18. SELECT * from t1,t2
19. WHERE t1.HADM_ID = t2.HADM_ID

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（4）首次进ICU时年龄不小于18岁的高血压患者

1. with t1 as(
2.     -- 用age和icustay_detail两个物化视图
3.     select i.subject_id, i.hadm_id, i.stay_id, ROUND(a.age,0) as age
4.     from icustay_detail as i
5.     LEFT JOIN age as a
6.     ON i.first_icu_stay = 't'and i.hadm_id = a.hadm_id and a.age>=18
7. ),
8. t2 as (
9. -- 查看高血压的患者
10. SELECT DISTINCT (HADM_ID)
11. FROM MIMICIV_HOSP.DIAGNOSES_ICD
12. WHERE ICD_CODE = '4019' and ICD_VERSION = 9
13. )
15. SELECT * from t1,t2
16. WHERE t1.HADM_ID = t2.HADM_ID

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（5）首次进ICU时年龄不小于18岁的脑梗患者

1. with t1 as(
2.     -- 用age和icustay_detail两个物化视图
3.     select i.subject_id, i.hadm_id, i.stay_id, ROUND(a.age,0) as age
4.     from icustay_detail as i
5.     LEFT JOIN age as a
6.     ON i.first_icu_stay = 't'and i.hadm_id = a.hadm_id and a.age>=18
7. ),
8. t2 as (
9. -- 脑梗患者
10. SELECT d.subject_id,d.hadm_id
11. from mimiciv_hosp.diagnoses_icd d
12. WHERE d.icd_code in ('43301','43330','43331','43390','43391','G43609','43411','I630','I63012','I63013','I6302','I63032','I63033','I63039','I6309','I631','I6310','I63111','I63112','I63113','I63139','I632','I6320','I63212','I63213','I63219','I6322','I63231','I63232','I6330','I63311','I63312','I63319','I6332','I63321','I63322','I63339','I6334','I63341','I63342','I63343','I6339','I6341','I63411','I63412','I63413','I63419','I6342','I6343','I63431','I63432','I63433','I63441','I63442','I6350','I6351','I63511','I63512','I63513','I6352','I63521','I63529','I6353','I63531','I63532','I63541','I63542','I63549','I6359','I636','I69312','I69314','I69341','I69342','I69359','I69361','I69362','I69363','I69364')
13. )
14. SELECT t1.* from t1,t2
15. WHERE t1.HADM_ID = t2.HADM_ID

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保存到一个表里。

1. -- 创建并保存到新表icu_ci
2. CREATE TABLE icu_ci as (
3. with t1 as(
4.     -- 用age和icustay_detail两个物化视图
5.     select i.subject_id, i.hadm_id, i.stay_id, ROUND(a.age,0) as age
6.     from mimiciv_derived.icustay_detail as i
7.     LEFT JOIN mimiciv_derived.age as a
8.     ON i.first_icu_stay = 't'and i.hadm_id = a.hadm_id and a.age>=18
9. ),
10. t2 as (
11. -- 脑梗患者
12. SELECT d.subject_id,d.hadm_id
13. from mimiciv_hosp.diagnoses_icd d
14. WHERE d.icd_code in ('43301','43330','43331','43390','43391','G43609','43411','I630','I63012','I63013','I6302','I63032','I63033','I63039','I6309','I631','I6310','I63111','I63112','I63113','I63139','I632','I6320','I63212','I63213','I63219','I6322','I63231','I63232','I6330','I63311','I63312','I63319','I6332','I63321','I63322','I63339','I6334','I63341','I63342','I63343','I6339','I6341','I63411','I63412','I63413','I63419','I6342','I6343','I63431','I63432','I63433','I63441','I63442','I6350','I6351','I63511','I63512','I63513','I6352','I63521','I63529','I6353','I63531','I63532','I63541','I63542','I63549','I6359','I636','I69312','I69314','I69341','I69342','I69359','I69361','I69362','I69363','I69364')
15. )
16. SELECT t1.* from t1,t2
17. WHERE t1.HADM_ID = t2.HADM_ID
18. )

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数据表icu_ci在哪儿？看选定的组件。
 

 

 
 
三、MIMIC IV数据合并和洗濯

1 数据变量

研究主题：甘油三脂葡萄糖指数与肾脏疾病的关联性
确定提取哪些数据呢？如下。
变量名称表名subject_id病人编号mimiciv_derived.icustay_detailhadm_id住院编号mimiciv_derived.icustay_detailstay_idICU编号mimiciv_derived.icustay_detailage年龄mimiciv_derived.ageintimeICU进入时间mimiciv_derived.icustay_detailgender性别mimiciv_derived.icustay_detailheight身高mimiciv_derived.heightweight体重mimiciv_derived.weightBMI体质指数-GCS神经体系功能评分mimiciv_derived.gcsrbc红细胞mimiciv_derived.complcreatinine肌酐mimiciv_derived.chemistryrenal_disease肾脏病mimiciv_derived.charlsonTriglyceride甘油三酯mimiciv_hosp.labeventsglucose葡萄糖mimiciv_derived.chemistryTyGTyG指数-- 2 数据合并

新建schema框架，用以保存我们处理的数据。

1. DROP SCHEMA IF EXISTS work CASCADE;
2. CREATE SCHEMA work;

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更多内容和课程资料在公众号！
五 小结

• （1）MIMIC数据分析研究发起。
  

一是做好数据检查，有没有遗漏、有没有重复、有没有多删或少删。基础数据（如首次不小于18岁），然后用left join逐个提取合并。合并前后的数据量变革，一定要做好检查。
二是数据提取用SQL完成，数据洗濯与分析用R。对于提取时间很长的数据，如实验数据（甘油三酯）、药品数据等，可把初始数据提取后保存为一个表，后面必要处理用这个表就行。
三是熟悉研究的基本思路，如数据纳排（按了局变量、自变量、协变量的序次）作为数据选取流程图的依据，是论文的一部门，另有数据格式转化、分类变量等。另外，MIMIC数据分析不涉及权重，与NHANES不同。

• （2）课程福利。
  
• （3）课程资料获取。课程资料包罗[DAY1]SCI论文复现全部代码-基于R、PostgreSql/Navicat等软件、SQL常用下令与批处理脚本、课本;[Day2]MIMIC IV常见数据提取代码-基于sql、数据洗濯-基于R课本；[Day3] 待更新[Day4]待更新等。关注公众号“熊大学习社”，复兴“mimic01”，获取全部MIMIC复现课程资料链接。
  

 

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